μCaler RIA Solution for Respiratory Pathogen Identification and AMR Analysis

Pathogen Species List

Classiﬁcation		Pathogen
Virus（35 species）	DNA virus (12 species)	Human polyomavirus 1 (BK Polyomavirus), Human polyomavirus 2 (JC Polyomavirus), Human polyomavirus 4 (WU Polyomavirus), Human adenovirus B/C/D, Human Alphaherpesvirus 1/2/3, Human Gammaherpesvirus 4 (Epstein-Barr Virus), Human Betaher-pesvirus 5/6/7, Human Bocavirus 1/2/3/4, Human Parvovirus B19, Monkeypox Virus
	RNA virus (23 species)	Human Rhinovirus A/B/C, Human Respiratory Syncytial Virus A/B, Human Parainﬂuenza Virus 1/3, Human Parainﬂuenza Virus 2/4, Mumps Virus, Inﬂuenza A virus (coverage of encoding genes), Inﬂuenza B, Inﬂuenza C, Coxsackievirus A/B, Echovirus, Enterovirus A71/D68, Human Metapneumovirus, Measles Virus Genotype D8, Rubella Virus Genotype 2B, SARS-CoV, SARS-CoV-2 (coverage of whole genome), MERS, Human Coronavirus (OC43, HKU1), Human Coronavirus (229E, NL63)
Bacteria (> 146 species)		E. coli, S. aureus, S. epidermidis, S. haemolyticus, K. pneumoniae, A. baumannii, A. junii, P. aeruginosa, S. maltophilia, P. micra, S. pneumoniae, S. dysgalactiae, S. inter-madius, S. anginosus, S. constellatus, S. pyogenes, S. agalactiae (group B streptococcus or GBS), P. anaerobius, M. tuberculosis, M. bovis, M. africanum, M. canetti, M. leprae, M. avium, M. intracellulare, M. abscessus, M. chelonae, M. malmoense, M. xenopi, M. scrofulaceum, M. kansasii, M. fortuitum, M. marinum, M. haemophilum, M. szulgai, M. simiae, M. asiaticum, M. smegmatis, M. shottsii, M. genavense, M. gordonae, M. ulcerans, M. novum, M. neoaurum, M. botniense, M. chimaera, M. mantenii, M. heckeshornense, M. interjectum, M. intermedium, Candidatus M. methanotrophicum, M. alsense, M. angelicum, M. aquaticum, M. bouchedurhonense, M. bourgelatii, M. branderi, M. celatum, M. conspicuum, M. europaeum, M. fragae, M. kubicae, M. kyorinense, M. lacus, M. lehmannii, M. monteﬁorense, M. noviomagense, M. ostraviense, M. palustre, M. paraense, M. paragordonae, M. paraseoulense, M. paraterrae, M. parmense, M. persicum, M. seoulense, M. sherrisii, M. shigaense, M. shimoidei, M. shin-jukuense, M. simulans, M. spongiae, M. stomatepiae, M. talmoniae, M. tilburgii, M. timonense, M. vicinigordonae, M. yunnanensis, N. gonorrhoeae, N. meningitidis, B. anthracis, B. cereus, B. fragilis, C. freundii, A. haemolyticum,C. diphtheriae , C. pseudotuberculosis, F. necrophorum, H. inﬂuenzae, H. parainﬂuenzae, S. marcescens, M. catarrhalis, B. pertussis, B. parapertussis, B. bronchiseptica, B. holmesii, L. pneumophila, E. meningoseptica, E. anophelis, C. burnetii, B. abortus, B. anthropi, B. melitensis,B. canis, B. Suis, L. monocytogenes, Y. pestis, Y. enterocolitica, N. otitidiscaviarum, N. nova, N. asteroides, N. farcinica, N. brasiliensis, N. pneumoniae, N. abscessus, N. arthritidis, N. beijingensis, N. cyriacigeorgica, N. transvalensis, N. veterana, V. parahaemolyticus, S. enterica, E. faecium, E. faecalis, E. cloacae, P. mirabilis, P. vulgaris, P. intermedia, P. melaninogenica, V. parvula, F. magna, L. interrogans, T. pallidum, B. quintana, B. henselae, B. cepacia
Fungi (41 species)		P. jirovecii, C. neoformans, C. gattii, T. asahii, C. albicans, C. tropicalis, C. dubliniensis, C. parapsilosis, C. lusitaniae, C. glabrata, C. krusei, C. auris, A. ﬂavus, A. fumigatus, A. niger, A. terreus, A. nidulans, A. versicolor, H. capsulatum, R. arrhizus, R. microsporus, R. oryzae, R. pusillus, M. circinelloides, M. indicus, M. racemosus, L. ramosa, L. corymbifera, C. bertholletiae, T. marneﬀei, C. immitis, P. variotii, P. lilacinum, L. proliﬁcans, L. valparaisensis, A. alternata, A. infectoria, S. boydii, S. apiospermum, F. solani complex, F. oxysporum complex
Other pathogens (4 species)		M. pneumoniae, C. pneumoniae, C. psittaci, C. trachomatis

AMR Markers List

Pathogen		Antimicrobial Resistance (AMR)
Classfication	Species	Type	Mechanism	Gene
Bacteria	Acinetobacter baumannii Enterococcus faecalis Enterococcus faecium Escherichia coli Haemophilus influenzae Haemophilus parainfluenzae Klebsiella pneumoniae Listeria monocytogenes Pseudomonas aeruginosa Salmonella enterica Staphylococcus aureus Streptococcus pneumoniae ......	Aminoglycosides	Antibiotic Inactivation	AAC(2'), AAC(3), AAC(6'), AAC(6')-Ie-APH(2'')-Ia, ANT(2''), ANT(3''), ANT(4'), APH(2''), APH(3'), APH(3’’), APH(6)
		Aminoglycosides	Antibiotic Target Alteration	armA, rmtA, rmtB, rmtD
		Penicillins Cephalosporins Carbapenems	Antibiotic Inactivation	ACC, ACT, CMY, DHA, Abau_ampC_BLA, Ecol_ampC_BLA, TEM, SHV, CTX-M, PER, GES, SME, VEB, IMI, NmcA, NmcR, KPC, OXA, GIM, IMP, SFH, SPM, VIM, NDM, IND
			Antibiotic Target Alteration	PBP1a, PBP2, PBP2x, PBP3
			Antibiotic Target Replacement	mecA, mecC
			Reduced Permeability to Antibiotic	ompF, oprD
		Peptides	Antibiotic Target Alteration	MCR, basR, PhoP, PhoQ, LpxA, LpxC, cls, mprF, pgsA, walK, menA, vanA, vanB, vanC, vanD, vanG
		Fluoroquinolones	Antibiotic Target Protection	QnrA1, QnrB1, QnrB4, QnrS1
			Antibiotic Target Alteration	gyrA, gyrB, parC, parE
			Antibiotic Efflux Pumps	PatA, PatB, PmrA
		Aminocoumarins	Antibiotic Target Alteration	gyrB
		Macrolides	Antibiotic Inactivation	EreA, EreB, mphB
			Antibiotic Target Alteration	ErmA, ErmB, ErmF
			Antibiotic Target Protection	msrA, mel
		Lincosamides Streptogramins	Antibiotic Target Alteration	ErmA, ErmB, ErmF
		Chloramphenicols	Antibiotic Inactivation	catB3, catB8, Paer_catB6
		Chloramphenicols	Antibiotic Efflux Pumps	cmlA
		Tetracyclines	Antibiotic Target Protection	tet(M), tet(Q), tet(T), tet(W)
		Tetracyclines	Antibiotic Efflux Pumps	tet(A), tet(D)
		Sulfonamides	Antibiotic Target Alteration	folP
		Nitrofurans	Antibiotic Inactivation	nfsA
		Rifamycins	Antibiotic Target Alteration	rpoB, rpoC
		MDR	Antibiotic Efflux Pumps	mtrC, mtrD, mtrE, AcrF, TolC, emrA, adeB, adeF, oqxA, oqxB, qacA, mdfA, acrR, ramR, soxS, soxR
Fungi	Candida albicans Candida parapsilosis Candida glabrata Candida auris Cryptococcus neoformans Cryptococcus gattii Aspergillus fumigatus	Azoles	Antibiotic Target Alteration	ERG11, CYP51A, CYP51C
			Antibiotic Target Overexpression	Upc2, hapE, Hmg1
			Efflux Pump Overexpression	TAC1, MRR1, PDR1
			Antibiotic Inactivation	ERG3
		Echinocandins	Antibiotic Target Alteration	FKS1, FKS2
		Polyenes	Antibiotic Target Absence	ERG11
		Pyrimidines	Reduced Permeability to Antibiotic	FCY2, UXS1

Application

Upper respiratory tract infections (URTIs): common cold, influenza, rhinitis, pharyngitis, tonsillitis, laryngitis, etc.
Lower respiratory tract infections (LRTIs): tracheitis, bronchitis, bronchiectasis, bronchiolitis, pneumonia, lung abscess, etc
Mycobacterial infections: pulmonary tuberculosis and nontuberculous mycobacteria (NTM) lung disease, etc.
Chronic respiratory infections: chronic obstructive pulmonary disease (COPD), asthma, etc.

Applicable for the detection of respiratory specimens, including oropharyngeal/nasopharyngeal swabs, sputum, bronchoalveolar lavage fluid/bronchial washing fluid, pleural fluid/ascites, and lung biopsy tissue.

Workflow

Feature

Sample-in, result-out; TAT reduced to 12 hr.
> 99% common clinical pathogens + ~200 AMR markers.
Specific detection of low-load pathogens with stable, reliable results.
End-to-end QC to reduce false positives.
AMR markers identification with source-microbes attribution.
Fine-resolution genotyping and variant analysis for key RNA viruses.

Performance

Stable Detection of Multiple Pathogens in Reference Standard

Table 1. Limit of detection (LoD) of the μCaler RIA Solution for multiple pathogens in reference standard.

A total of 0.4 mL of reference standard at diﬀerent concentration gradients was used for extraction of mixed RNA & DNA. Pre-libraries were prepared using the NadPrep EZ RNA & DNA Library Co-Preparation Module coupled with the NadPrep Universal Stubby Adapter (UDI) Module. Hybrid capture was performed using the μCaler HyperMix Hybrid Capture Kit (for Illumina®) and the μCaler RIA Panel v1.0. Sequencing was performed on MiSeq with PE150, with raw data of 3 M read pairs per sample.

Note: RPM stands for reads per million mapped reads.

Signiﬁcantly Improved Detection Rate for Clinically Important Pathogens

Figure 1. Heatmap comparison of detection concordance among the μCaler RIA Solution, mNGS, and culture for key clinical pathogens.

Note: Light blue and light gray blocks indicate positive and negative results, respectively; white block indicates the method is not applicable, and no valid result could be obtained. Samples were collected from 78 clinical patients, including multiple specimen types such as sputum and BALF. Clinically important pathogens included in the analysis were: MTBC (M. tuberculosis complex), NTM (nontuberculous mycobacteria), Nocardia spp., P. jirovecii, A. fumigatus, and C. neoformans.

Precise Identiﬁcation of Antimicrobial Resistance Genes (ARGs) and Associated Pathogens

Table 2. Concordance analysis between the μCaler RIA Solution and conventional methods for pathogens detection and distribution of ARGs across diverse clinical specimens.

For research use only. Not for use in diagnostic procedures.

Lib Prep Module

Packing No.	Color of Tube Cap	Component	Volume 1002451 (24 rxn)	Volume 1002452 (96 rxn)
Box1		Co-Random Primer	90 µL	350 µL
		cDNA Synth. Mix	435 µL	2×875 µL
		Co-FERA Mix	250 µL	980 µL
		Co-Ligation Mix	600 µL	2×1,200 µL
		2X HiFi PCR Master Pro Mix	1,300 µL	4×1,300 µL
		PCR Enhancer (for Illumina^®)	150 µL	575 µL
		PCR Enhancer (for MGI, DI)	150 µL	575 µL
	/	Nuclease Free Water	2.5 mL	8 mL
		TE Solution	1 mL	4 mL
Box2	/	NadPrep SP Beads	4 mL	15 mL

Universal Stubby Adapter (UDI) Module

Color of Tube Cap	Component	Volume 1003240 (24 rxn)	Volume 1003241 (96 rxn)	Volume 1003242 (96 rxn)
	NadPrep Universal UDI-index Primer Mix #	12×15 µL (Tube)	24×25 µL (Tube)	24×25 µL (Tube)
	NadPrep Universal Stubby Adapter	60 µL (Tube)	230 µL (Tube)	230 µL (Tube)
	NadPrep Amplification Primer Mix II	20 µL (Tube)	75 µL (Tube)	75 µL (Tube)

Color of Tube Cap	Component	Volume 1003251 (96 rxn)	Volume 1003252 (96 rxn)	Volume 1003253 (96 rxn)	Volume 1003254 (96 rxn)
Color of Tube Cap	Component	Volume 1003251 (96 rxn)	Volume 1003252 (96 rxn)	Volume 1003253 (96 rxn)	Volume 1003254 (96 rxn)
	NadPrep Universal UDI-index Primer Mix #	96×8 µL (Plate)	96×8 µL (Plate)	96×8 µL (Plate)	96×8 µL (Plate)
	NadPrep Universal Stubby Adapter	260 µL (Tube)	260 µL (Tube)	260 µL (Tube)	260 µL (Tube)
	NadPrep Amplification Primer Mix II	75 µL (Tube)	75 µL (Tube)	75 µL (Tube)	75 µL (Tube)

Color of Tube Cap	Component	Volume 1003255 (96 rxn)	Volume 1003256 (96 rxn)	Volume 1003257 (96 rxn)	Volume 1003258 (96 rxn)
Color of Tube Cap	Component	Volume 1003255 (96 rxn)	Volume 1003256 (96 rxn)	Volume 1003257 (96 rxn)	Volume 1003258 (96 rxn)
	NadPrep Universal UDI-index Primer Mix #	96×8 µL (Plate)	96×8 µL (Plate)	96×8 µL (Plate)	96×8 µL (Plate)
	NadPrep Universal Stubby Adapter	260 µL (Tube)	260 µL (Tube)	260 µL (Tube)	260 µL (Tube)
	NadPrep Amplification Primer Mix II	75 µL (Tube)	75 µL (Tube)	75 µL (Tube)	75 µL (Tube)

Color of Tube Cap	Component	Volume 1003261 (1152 rxn)	Volume 1003262 (1152 rxn)	Volume 1003263 (1152 rxn)	Volume 1003264 (1152 rxn)
Color of Tube Cap	Component	Volume 1003261 (1152 rxn)	Volume 1003262 (1152 rxn)	Volume 1003263 (1152 rxn)	Volume 1003264 (1152 rxn)
	NadPrep Universal UDI-index Primer Mix #	96×72 µL (Tube)	96×72 µL (Tube)	96×72 µL(Tube)	96×72 µL (Tube)
	NadPrep Universal Stubby Adapter	2×1,350 µL (Tube)	2×1,350 µL (Tube)	2×1,350 µL (Tube)	2×1,350 µL (Tube)
	NadPrep Amplification Primer Mix II	900 µL (Tube)	900 µL (Tube)	900 µL (Tube)	900 µL (Tube)

MDI Adapter Module (for MGI)

Color of Tube Cap	Component	Volume 1003711 (24 rxn)	Volume 1003721 (96 rxn)	Volume 1003722 (96 rxn)	Volume 1003725 (96 rxn)	Volume 1003726 (96 rxn)
	NadPrep M-Index (MDI) Primer Mix #	12×15 µL (Tube)	24×25 µL (Tube)	24×25 µL (Tube)	24×25 µL (Tube)	24×25 µL (Tube)
	NadPrep M-Adapter (DI)	60 µL (Tube)	230 µL (Tube)	230 µL (Tube)	230 µL (Tube)	230 µL (Tube)

Color of Tube Cap	Component	Volume 1003751 (96 rxn)	Volume 1003752 (96 rxn)	Volume 1003753 (96 rxn)	Volume 1003754 (96 rxn)
Color of Tube Cap	Component	Volume 1003751 (96 rxn)	Volume 1003752 (96 rxn)	Volume 1003753 (96 rxn)	Volume 1003754 (96 rxn)
	NadPrep M-Index (MDI) Primer Mix #	96×8 µL (Plate)	96×8 µL (Plate)	96×8 µL (Plate)	96×8 µL (Plate)
	NadPrep M-Adapter (DI)	260 µL (Tube)	260 µL (Tube)	260 µL (Tube)	260 µL (Tube)
	NadPrep M-Amplification Primer Mix (for MGI, DI)	75 µL (Tube)	75 µL (Tube)	75 µL (Tube)	75 µL (Tube)

Color of Tube Cap	Component	Volume 1003761 (1152 rxn)	Volume 1003762 (1152 rxn)	Volume 1003763 (1152 rxn)	Volume 1003764 (1152 rxn)
Color of Tube Cap	Component	Volume 1003761 (1152 rxn)	Volume 1003762 (1152 rxn)	Volume 1003763 (1152 rxn)	Volume 1003764 (1152 rxn)
	NadPrep M-Index (MDI) Primer Mix #	96×8 µL (Plate)	96×8 µL (Plate)	96×8 µL (Plate)	96×8 µL (Plate)
	NadPrep M-Adapter (DI)	2×1,350 µL (Tube)	2×1,350 µL (Tube)	2×1,350 µL (Tube)	2×1,350 µL (Tube)
	NadPrep M-Amplification Primer Mix (for MGI, DI)	900 µL (Tube)	900 µL (Tube)	900 µL (Tube)	900 µL >(Tube)

Hybrid Capture Reagents (for Illumina®)

Color of Tube Cap	Component	Volume 1105302 (16 rxn)	Volume 1105301 (96 rxn)
Color of Tube Cap	Component	Volume 1105302 (16 rxn)	Volume 1105301 (96 rxn)
	μHybCap HyperMix (for Illumina^®)	890 μL	3×1,770 µL
	μEnhancer	1,300 μL	8 mL
	Hyper Streptavidin Beads	160 μL	920 μL
/	Wash Buffer A Pro	5.8 mL	2×17.5 mL
/	Wash Buffer B	2.9 mL	20 mL

Hybrid Capture Reagents (for MGI)

Color of Tube Cap	Component	Volume 1105402 (16 rxn)	Volume 1105401 (96 rxn)
Color of Tube Cap	Component	Volume 1105402 (16 rxn)	Volume 1105401 (96 rxn)
	μHybCap HyperMix (for MGI)	890 μL	3×1,770 µL
	Hyper Streptavidin Beads	160 μL	920 μL
/	Wash Buffer A Pro	5.8 mL	2×17.5 mL
/	Wash Buffer B	2.9 mL	20 mL

Panel

Color of Tube Cap	Component	Volume	Package/Storage

	μCaler RIA Panel v1.0，96 rxn	210 μL	-25~-15℃

For research use only. Not for use in diagnostic procedures.

Type	Product	Detail	Catalog#
Lib Prep Module	NadPrep EZ RNA & DNA Library Co-Preparation Module v2, 24 rxn	24 rxn	1002451
Lib Prep Module	NadPrep EZ RNA & DNA Library Co-Preparation Module v2, 96 rxn	96 rxn	1002452
Universal Stubby Adapter (UDI) Module	NadPrep Universal Stubby Adapter (UDI) Module Set A1, 24 rxn	Index 1-12	1003240
	NadPrep Universal Stubby Adapter (UDI) Module Set B1, 96 rxn	Index 1-24	1003241
	NadPrep Universal Stubby Adapter (UDI) Module Set B2, 96 rxn	Index 25-48	1003242
	NadPrep Universal Stubby Adapter (UDI) Module Set E1, 96 rxn	Index 1-96	1003251
	NadPrep Universal Stubby Adapter (UDI) Module Set E2, 96 rxn	Index 97-192	1003252
	NadPrep Universal Stubby Adapter (UDI) Module Set E3, 96 rxn	Index 193-288	1003253
	NadPrep Universal Stubby Adapter (UDI) Module Set E4, 96 rxn	Index 289-384	1003254
	NadPrep Universal Stubby Adapter (UDI) Module Set E5 , 96 rxn	Index 385-480	1003255
	NadPrep Universal Stubby Adapter (UDI) Module Set E6 , 96 rxn	Index 481-576	1003256
	NadPrep Universal Stubby Adapter (UDI) Module Set E7 , 96 rxn	Index 577-672	1003257
	NadPrep Universal Stubby Adapter (UDI) Module Set E8 , 96 rxn	Index 673-768	1003258
	NadPrep Universal Stubby Adapter (UDI) Module Set F1, 1152 rxn	Index 1-96	1003261
	NadPrep Universal Stubby Adapter (UDI) Module Set F2, 1152 rxn	Index 97-192	1003262
	NadPrep Universal Stubby Adapter (UDI) Module Set F3, 1152 rxn	Index 193-288	1003263
	NadPrep Universal Stubby Adapter (UDI) Module Set F4, 1152 rxn	Index 289-384	1003264
MDI Adapter Module (for MGI)	NadPrep Universal Adapter (MDI) Module Set A1 (for MGI), 24 rxn	MDI 1-12	1003711
	NadPrep Universal Adapter (MDI) Module Set B1 (for MGI), 96 rxn	MDI 1-24	1003721
	NadPrep Universal Adapter (MDI) Module Set B2 (for MGI), 96 rxn	MDI 25-48	1003722
	NadPrep Universal Adapter (MDI) Module Set B3 (for MGI), 96 rxn	MDI 49-72	1003725
	NadPrep Universal Adapter (MDI) Module Set B4 (for MGI), 96 rxn	MDI 73-96	1003726
	NadPrep Universal Adapter (MDI) Module Set E1 (for MGI), 96 rxn	MDI 1-96	1003751
	NadPrep Universal Adapter (MDI) Module Set E2 (for MGI), 96 rxn	MDI 97-192	1003752
	NadPrep Universal Adapter (MDI) Module Set E3 (for MGI), 96 rxn	MDI 193-288	1003753
	NadPrep Universal Adapter (MDI) Module Set E4 (for MGI), 96 rxn	MDI 289-384	1003754
	NadPrep Universal Adapter (MDI) Module Set F1 (for MGI), 1152 rxn	MDI 1-96	1003761
	NadPrep Universal Adapter (MDI) Module Set F2 (for MGI), 1152 rxn	MDI 97-192	1003762
	NadPrep Universal Adapter (MDI) Module Set F3 (for MGI), 1152 rxn	MDI 193-288	1003763
	NadPrep Universal Adapter (MDI) Module Set F4 (for MGI), 1152 rxn	MDI 289-384	1003764
Hybrid Capture Reagents	μCaler HyperMix Hybrid Capture Kit (for Illumina®), 16 rxn	16 rxn	1105302
	μCaler HyperMix Hybrid Capture Kit (for Illumina®), 96 rxn	96 rxn	1105301
	μCaler HyperMix Hybrid Capture Kit (for MGI), 16 rxn	16 rxn	1105402
	μCaler HyperMix Hybrid Capture Kit (for MGI), 96 rxn	96 rxn	1105401
Panel	μCaler RIA Panel v1.0, 96 rxn	96 rxn	1101451
Visual Platform	XCapViz Bioinformatics Analysis Visual System	Unit	1009101
Automated Reporting	Prebuilt Pipelines (RIA)	Unit	1009102